


Until the Smoke Clears

by cathydeff



Category: Marvel Cinematic Universe, The Avengers (Marvel Movies)
Genre: Alpha/Beta/Omega Dynamics, Emotional Torture (mentioned), Genital Mutilation (mentioned), Howard Stark's A+ Parenting, M/M, Medical Experimentation, No beta we die like mne
Language: English
Status: Completed
Published: 2018-12-22
Updated: 2018-12-22
Packaged: 2019-09-24 10:05:10
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 2,778
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/17098562
Author URL: https://archiveofourown.org/users/cathydeff/pseuds/cathydeff
Summary: Tony was born an omega, but Howard, in shame, turns him into a beta.After the fight at Johannesburg with the Hulk, Bruce & Cho inject Tony with experimental nanites to save his life. It works, but he’s also physically 21, turned back into his original omega gender, and is now apparently Captain America’s scent mate.Captain America, who’s never noticed that Tony was interested, and then some.Fuck his life.





	Until the Smoke Clears

**Author's Note:**

  * For [RawWriting](https://archiveofourown.org/users/RawWriting/gifts).



> Done as pinch hit for the Cap IM Holiday Exchange, and as there was a deadline I wanted to accomplish to make sure my giftee does get something for the exchange, this was churned out. I took out bits of the prompt and worked with my brain wanted as much as possible, but I hope this still entertains! Might go back to expand on this universe as it was quite fun to write.

When Tony wakes up, all he can feel is pain. The only thing that really doesn’t hurt are his eyelids—his skin feels stretched and taut, his muscles sore, and his head aching like someone hit him in the head.

He remembers what happened at Johannesburg. With the Hulk and the Hulkbuster. And millions of dollars worth of destruction. And lives taken and hurt.

Shit.

He tries to sit up, but his body protests strongly, the pain making itself known in places it didn’t hurt before. Whatever they had him on, he needed another dose stat.

“I would stay down if I were you,” a voice says from beside him and he starts, pulling a sore rib.

“What’s happened to me, Doc?” Tony groans, lying back down. If Bruce is here, it means the Hulk was subdued.

“You were seriously injured,” Bruce explains, avoiding his eye. Tony can sense the guilt coming off in waves from the other scientist.

“Bruce, whatever you’re thinking, that this is your fault, can it,” Tony says with a tone of finality. “Everyone was mind-whammied, and the Hulk hasn’t really learned the finer points of control.” 

Tony gave his toes an experimental wiggle, but for some reason, the pain is receding somewhat, and did Bruce up his morphine without him knowing?

Bruce bit his lip before saying, “I know that. The team has told me that. But still…” he sighed. “You were in a bad shape, Tony.” He takes his glasses off, rubs his eyes before continuing. “Helen and I—even the cradle wasn’t working fast enough to prevent complete organ shutdown with the damage you took!” 

Bruce collapses on the chair by Tony again, and Tony stares at him, fearing the worst. This was it, wasn’t it. He’s going to die. But...there was a lot of things he hasn’t done yet! Hasn’t even...told him anything yet, never got the chance to ask him for a coffee or anything like that and see where it took them. He was finally going to be brave. 

Tony swallows, not knowing how to comfort his friend but dread consumes him. 

“We had to take drastic action,” Bruce whispers. “Remember that nanite project you and I were working on?”

Tony doesn’t answer, and forces himself up. The pain is no longer evident, and he can move freely. With that realisation, he grits his teeth.

“What did you do?” Tony demands. He clenches his fist but can’t help but notice that they look different. 

“We injected you with the nanites,” Bruce admits, his voice tiny and soft. “It worked. Your body accepted the nanite and they started to repair your body faster than the cradle ever could.” 

Tony springs up from the bed, and stares at himself in the mirror in the bathroom. He looks like him—only twenty years younger.

“The nanites also regressed your age,” Bruce explains. Tony looks at his hands, unscarred, his face devoid of his customary wrinkles. His hair had lost its grey tinge and is now dark and full. His body no longer had the normal aches and pains due to aging and half a lifetime of debauchery.

“According to the scans, you’re 21 again.”

Tony can’t help it. He screams.

—

Bruce paces the floor in front of him, while Cho is at the screens, taking notes of Tony’s scans.

“This is—this is more than we ever expected from the project,” Bruce babbles, his face flush with excitement. Tony scowls at him, but he cannot be deterred. “We were only hoping for something like enhanced healing in battle but for you to regress, this is amazing!”

“The cellular regeneration is truly spectacular,” pipes up Cho. “From the looks of it, you are aging at a slower rate than normal, and this could extend your lifespan by a good few decades, at least.”

Tony’s nose flares; he wants to snap at them but can understand how exciting this is from a scientific view. However, it is his body that was just willy nilly used as a guinea pig—sure it saved his life, but there’s ethics and shit!

Tony pulls one of the screens closer to him, and sees a small note in the corner.

“Bruce, why does this say that my secondary gender is now an omega?” Tony calls out in a sing song manner, not betraying the panic and fear in his gut. 

“Ah, yeah, we were going to get into that,” Bruce intones. “We were quite confused as to how you went from a beta to an omega but it could be due to the nanites.”

Tony nods. “Makes sense,” he says, then vomits on the floor.

——

“Tony! Let us in! What’s wrong?” Bruce yells from the other side of the bathroom door, jiggling the knob.

Tony is curled up on the floor, his head between his knees, his breathing coming in short pants. 

“Fuck you, Banner! Leave me the fuck alone!” Tony screams back. He thumps his head against the door and contemplates the likelihood of him drowning in the small sink. 

“I will Hulk out and break down this damn door if I have to, Tony!” Bruce threatens.

“Piss off!”

Bruce sighs, leans his head on the door, and pleads, “I’m sorry, Tony, but I’m your friend, you need to tell me what’s the matter. We’re worried.”

“If you are my friend you would have left me to die when Hulk beat the shit out of me and ruined my billion dollar suit!”

“Tony!”

Tony gets up fiercely—his joints no longer creak—and opens the door. 

“Fine, you know what’s wrong?” Tony seethes, his knuckles white with how hard he was clenching his fists. “Howard. He could not accept an omega son, he wanted an Alpha, but even a beta would do. Have you heard of Project Oyster?”

Bruce’s eyes widen in shock. He nods slowly, knowing of the illegal experimentation in the 60’s, wherein unwilling omegas were kidnapped from the streets by an unknown organisation and had forcible gender reassignment. Some were turned into Alphas but the majority were betas. Almost all of the victims could not handle the sudden change, and some killed themselves or went on a killing spree, blaming the world. The rest were in mental institutions for the rest of their lives.

“Well, didn’t you know that Howard knew one of the psychos who did that crap,” Tony’s voice was dangerously low, a tremble and a hitch at points. 

“No, Tony, please don’t tell me…”

“Howard had an omega son. He turned him into a beta—the best they could do at that time. He...he stitched me up, put an implant in me so I emitted beta pheromones...he took away my—my parts—“ Tony can no longer continue and as he is about to sink to the floor again in tears, Bruce catches him, holds him tight and he can feel the sobs wracking Bruce’s body as well as his own.

“Tony, I am so sorry, Tony, I didn’t know, forgive me,” Bruce repeats over and over, pressing Tony’s face into his shoulder.

“What’s going on here?” Another voice comes into the medi bay. “Helen went to come and get me. Is Tony okay? Is he finally out of the cradle? Bruce?”

Fuck. Tony tries to wriggle away from Bruce but Bruce keeps him where he is. Tony can easily overpower him in his younger body but relishes the warmth his friend emanates. As a—fellow—omega, Bruce understood, and his instincts are screaming that a friend is in trouble and in need of soothing.

“What’s that smell?” Steve says slowly, and Tony can imagine his nostrils flaring as he tries to locate the scent. Tony winces and pushes against Bruce again. The other man relents and lets go, wiping at his eyes beneath his glasses. 

“That’s me,” Tony confesses. “I—“

Steve _moves_ , quicker than either Tony or Bruce can register and he has Tony in his arms, his face buried in Tony’s neck.

“What—the—Steve! Let me go!” It’s no use, it’s like struggling against a brick wall. 

“Steve!” Bruce says, alarmed. 

Steve raises his head up, his normally blue eyes tinged Alpha red. 

“My omega,” he growls at Tony. “You smell like my omega.”

—

It took Dum-E wheeling along with a fire extinguisher and dousing the both of them before Steve would let Tony go, and Tony took the chance to run up to the elevator and then barricade himself in his bedroom in the penthouse. 

Tony runs to the bathroom as soon as he is in, and takes note of himself in the mirror. He wants to see what happened below, but he can’t make himself. It’s all so strange and frightening.

Then Steve had to scent him and declare him his omega.

Normally, Tony would have melted in a puddle. Who wouldn’t. He is the Alpha to end all Alphas. The man is perfection incarnate, and he has a great personality to boot. Tony had been psyching himself to ask him out for ages, flirting left and right, letting him know when he and Pepper were on the outs, everything.

But Captain Thick Brick didn’t take the hints and Tony accepted to himself that he wasn’t interested. So he befriended him, hanging out, having Steve draw in the couch while he worked on something in the lab. 

Yet, Tony wanted—wants—more, he can no longer deny that. His body gives a little shudder at the thrill of being—being _Steve’s_. 

Tony dresses but studiously ignores anything down below and just hikes his boxers up. There’s still work to do, that weird little girl with the witchy powers and her brother, Flash. Maybe with the Mind Stone in their possession, he can make everyone helmets that can disrupt her mind altering powers. 

Just as he is about to open the door, someone knocks from the other side. 

“Tony? It’s Steve,” Steve calls. “Can we talk?”

“JARVIS,” Tony hisses, “I thought the penthouse was on lockdown?”

“I’m sorry, sir,” JARVIS intones. “You did not specify such an order. You told me to lock the access of the elevator but the Captain used the fire exits.”

“Then make sure this door does not open with my say so, clear?”

“Yes, sir.”

“Go away, Steve,” Tony says loudly. “I don’t know what happened in the lab, but get it out of your system now.”

“No,” says Steve stubbornly. “I know what I smelt, and it was you. Tony...you’re my mate.” There was a note of wonder and reverence in his voice. “But, I thought you were a beta.” 

“Ask your mate, Howard,” Tony snipes, unable to help himself.

“What?” 

“I was born an omega,” Tony says quietly, but no doubt the super soldier can hear it. “Howard didn’t like it. Just before I presented before puberty, he took me to a vacation, he called it.” The acid in his voice can melt the door. “But it was for surgery. I was injected everyday with this cocktail of medication to change my hormones, then I had surgery to change everything down there. My opening was stitched closed I came back to my mother a beta. So, please, dear Captain, please forgive me for panicking out of my mind!”

“Tony, oh god, baby doll,” Steve says brokenly. The endearment makes something in Tony’s chest flare and he flicks up a screen so the hallway is in view. Steve is on the floor, his face buried in his hands. 

“Tony, please, I need to make sure you’re alright,” Steve mutters. 

“You just want to scent me again,” Tony accuses. 

“No, no, I just—I want to make sure you’re alright, and this is your friend talking, not your—my Alpha, Tony this is huge,” he finishes softly.

“I can’t, I lived with being a beta, with knowing that this is—was—me,” Tony whispers. 

“Goddamit, what were Bruce and Dr Cho thinking giving you nanites?” Steve demands, and there is anger in his voice. 

“I think you know the extent of my injuries,” starts Tony. “The cradle wasn’t healing me fast enough. Bruce and I were experimenting with nanites that could be injected into the bloodstream to accelerate healing. Bruce used it as a last ditch attempt to get me stable enough for surgery but it did more than that.”

“Yeah.”

“I’m 21 now, physically, and apparently, back to my omega status.” Tony throws his head back and had to laugh at that. _Fuck you, Howard, your beloved science screws you over even in death._

“I was so scared,” Steve admits. Tony can see him making himself more comfortable, leaning against the door and stretching his legs out. “I think I was near out of my mind with worry. Clint kept offering me Valium and Natasha was ready to stab me.”

“Why should you? I’m barely your teammate. I’m just a consultant.”

“For a genius, you’re dumb,” Steve says lightly. “I just told you, you’re my friend. I hang out with you, we share pizza late at night, you let me draw in your lab, and I taught Butterfingers how to throw a ball.”

Tony smiles at that. “He broke several equipment the other day. He only has foam balls now.”

Steve winces. “Sorry.”

“Don’t be.”

A comfortable silence stretches between them as they lean against the same door, small smiles on their faces. 

“Tony, would you like to go to dinner with me?” Steve says and Tony nearly chokes on his spit.

“What? Please tell me you’re kidding. Is this the hormones again?”

“No, it’s—I’ve been meaning to ask you for a while now,” Steve confides. “But you’re—you’ve been with a few people who are smoother than I am and I didn’t know where to start.”

Tony opens the door so abruptly that Steve falls on his back. Tony looks down at the super soldier sprawled on his feet, and sees the slight glint of red at seeing him.

“Steve. I’ve been flirting with you for six months. You didn’t notice,” Tony deadpans.

Steve scrambles to his feet and pats himself down.

“I thought it was a thing you did,” Steve explains, shamefaced. “You seem to lay it on to whoever you had in front of you.”

“You calling me a slut?”

“Tony! Of course not! But you—you’re a showman, you’re used to laying on the charm for work, so I thought it was just another facet of you.” Steve smiles crookedly at him. “It didn’t matter to me, though, because I was the only one who ever got to see you conked out on your bench at three in the morning with pepperoni on your face.”

“Sorry, Cap, but that dubious honor goes to Rhodey,” Tony tsks. “MIT, eighties.”

Steve frowns at that, looking like a kicked puppy. 

“I’ll let you buy me a coffee, though, if you like.”

Steve perks up and nods. “Of course.”

“But not right now,” Tony hastily adds. “ There’s so much to do, I need to hold a press conference for the sudden change in my second gender, Pepper will have kittens and kill Bruce and Cho with her stilettos, and then stab me with her letter opener, and then there’s the Dynamic Duo who started all this nonsense with their creepy ass magic and this is not a fucking comic book—“

Steve stops his babbling by putting a hand across his mouth. Tony glares at him and contemplates licking his hand but it might enflame him. Steve’s smile is incandescent.

“One thing at a time, baby doll,” he says soothingly. “Coffee can wait, as long as I do get one.” His voices turns awestruck again. “And you, you’re my scent-mate.” The happiness of him is coming in waves. He looks like he dearly wanted to scent Tony again but desists. 

Tony removes his hand away from his face but doesn’t let go of his hand. He smiles back. Maybe something good can come out of this.

“Of course, Alpha,” he says cheekily, and takes pleasure at the flash of red in Steve’s eyes before the other man takes a deep breath to calm himself down.

“Word of warning, _omega_ ,” Steve says testily. “If you like what you’re wearing, do not call me that again.”

“Or what?”

Steve grins at him lazily, bringing up Tony’s hand to his mouth and presses a soft kiss to his knuckles. Tony certainly does not melt into a puddle of goo. Good lord, this man is determined to kill him. The nanites might not be enough next time to revive him.

“Would you like to find out?”

He very much would.


End file.
